Supplementary Methods, Supplementary Figures 1-10, Supplementary Tables 1-17, Supplementary References from Genome-Wide Association Study Identifies a New Locus at 7q21.13 Associated with Hepatitis B Virus–Related Hepatocellular Carcinoma

Supplementary Figure 1. An overview of the study workflow; Supplementary Figure 2. The principal components analyses (PCA) of samples in the discovery stage and reference samples from the 1000 Genomes Project data. Supplementary Figure 3. Manhattan plots of the genome-wide P values from the association tests on HBV-related HCC. Supplementary Figure 4. Quantile-quantile plots of the observed P values from the association tests on HBV-related HCC. Supplementary Figure 5. Forest plots for rs10272859 across all studies. Supplementary Figure 6. Expression levels of CDK14 mRNA were significantly higher in HCC tissues compared with adjacent non-tumor liver tissues. Supplementary Figure 7. The at-risk G allele of rs10272859 was significantly associated with higher mRNA levels of CDK14 in liver tissues based on the TCGA data. Supplementary Figure 8. The SNPs at 7q21.13 interact physically with the promoter region of CDK14 in GM12878 cells. Supplementary Figure 9. Kaplan-Meier estimates of the overall survival time for the HCC patients stratified by CDK14 mRNA expression levels. Supplementary Figure 10. Kaplan-Meier estimates of disease-free survival time for patients with HBV-related HCC stratified by genotypes of rs10272859. Supplementary Table 1. Summary description of the populations used in this study. Supplementary Table 2. Summary of the quality controls in proband-parent trios. Supplementary Table 3. Summary of SNP imputation in the discovery stage. Supplementary Table 4. The amount of SNPs with various P values in TDT for the 189 trios in the discovery stage. Supplementary Table 5. Summary of the SNPs that have been reported significantly associated with HBV-related HCC in previous GWASs. Supplementary Table 6. Summary of SNPs that have been reported to be significantly associated with HBV-related phenotypes in previous GWASs. Supplementary Table 6. Summary of SNPs that have been reported to be significantly associated with HBV-related phenotypes in previous GWASs (Continued). Supplementary Table 7. Summary of the top 15 SNPs in the discovery stage. Supplementary Table 8. Primers and probes used in this study. Supplementary Table 9. Summary of the replication studies for the 14 SNPs newly identified in the discovery stage. Supplementary Table 10. Stratification analyses of rs10272859 by gender and age. Supplementary Table 11. The associations between genotypes of rs10272859 and mRNA levels of nearby genes. Supplementary Table 12. The predicted functional relevance of rs10272859 and the other 74 SNPs in strong linkage disequilibrium with rs10272859 at the ~110 Kb region of 7q21.13. Supplementary Table 13. Details for the genotypes of rs10272859 and the prognosis of patients with HBV-related HCC. Supplementary Table 14. Multivariate analyses of overall survival time and disease-free survival time of patients with HBV-related HCC. Supplementary Table 15. Genotype distribution of rs10272859 across TNM stages in patients with HBV-related HCC. Supplementary Table 16. Powers for various genetic effects and various minor allele frequencies. Supplementary Table 17. The allele and genotype frequencies of rs10272859 in different populations.</p